RT Journal
A1 Xu, Han
A1 Xiao, Tengfei
A1 Chen, Chen-Hao
A1 Li, Wei
A1 Meyer, Clifford A.
A1 Wu, Qiu
A1 Wu, Di
A1 Cong, Le
A1 Zhang, Feng
A1 Liu, Jun S.
A1 Brown, Myles
A1 Liu, X. Shirley
T1 Sequence determinants of improved CRISPR sgRNA design
JF Genome Research 
JO Genome Research 
YR 2015 
FD August 01 
VO 25 
IS 8 
SP 1147 
OP 1157 
DO 10.1101/gr.191452.115 
UL http://genome.cshlp.org/content/25/8/1147.abstract 
AB The CRISPR/Cas9 system has revolutionized mammalian somatic cell genetics. Genome-wide functional screens using CRISPR/Cas9-mediated knockout or dCas9 fusion-mediated inhibition/activation (CRISPRi/a) are powerful techniques for discovering phenotype-associated gene function. We systematically assessed the DNA sequence features that contribute to single guide RNA (sgRNA) efficiency in CRISPR-based screens. Leveraging the information from multiple designs, we derived a new sequence model for predicting sgRNA efficiency in CRISPR/Cas9 knockout experiments. Our model confirmed known features and suggested new features including a preference for cytosine at the cleavage site. The model was experimentally validated for sgRNA-mediated mutation rate and protein knockout efficiency. Tested on independent data sets, the model achieved significant results in both positive and negative selection conditions and outperformed existing models. We also found that the sequence preference for CRISPRi/a is substantially different from that for CRISPR/Cas9 knockout and propose a new model for predicting sgRNA efficiency in CRISPRi/a experiments. These results facilitate the genome-wide design of improved sgRNA for both knockout and CRISPRi/a studies.